Blender adding extra bone when exporting FBX causes problems with Unity & Mixamo
I know it's a year late, but I've just had this same exact issue, so I would like to answer it here in case anyone else comes by this post.

The way to fix this in Unity is, after dragging the model into your scene, right clicking it and selecting 'unpack prefab'. Then, drag your hip object, that is parented by the unwanted armature node, up one level. You can then safely delete the armature node, and the animations should now work as normal.

Hope this will help some people, this behaviour isn't documented well enough for how annoying it is.